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- PDB-1zmm: Crystal structure of human alpha-defensin-4 -

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Basic information

Entry
Database: PDB / ID: 1zmm
TitleCrystal structure of human alpha-defensin-4
ComponentsNeutrophil defensin 4
KeywordsANTIMICROBIAL PROTEIN / HUMAN ALPHA-DEFENSIN / ANTIMICROBIAL PEPTIDE
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / Defensins / antifungal humoral response / antimicrobial humoral response / Alpha-defensins / azurophil granule / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen ...disruption of plasma membrane integrity in another organism / Defensins / antifungal humoral response / antimicrobial humoral response / Alpha-defensins / azurophil granule / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLubkowski, J. / Szyk, A. / Lu, W.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structures of human {alpha}-defensins HNP4, HD5, and HD6.
Authors: Szyk, A. / Wu, Z. / Tucker, K. / Yang, D. / Lu, W. / Lubkowski, J.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHOR STATES THE BIOLOGICAL UNIT IS A PROBABLE MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil defensin 4
B: Neutrophil defensin 4
C: Neutrophil defensin 4
D: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)14,8824
Polymers14,8824
Non-polymers00
Water1,874104
1
A: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)3,7201
Polymers3,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)3,7201
Polymers3,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)3,7201
Polymers3,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)3,7201
Polymers3,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.004, 39.255, 48.118
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide
Neutrophil defensin 4 / HNP-4 / HP-4 / Defensin / alpha 4


Mass: 3720.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFA4, DEF4 / Production host: Escherichia coli (E. coli) / References: UniProt: P12838
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, HEPES, 2-Methyl-2,4-pentanediol, PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 15948 / Num. obs: 15948 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.072 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.233 / % possible all: 71.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Based on the monomer of HNP-3 (PDB ID code 1DFN)

1dfn


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.67 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21791 806 5.1 %RANDOM
Rwork0.18545 ---
obs0.18707 15127 95.2 %-
all-15127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.366 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.07 Å2
2---0.39 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 0 104 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211025
X-RAY DIFFRACTIONr_bond_other_d0.0010.02986
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9861384
X-RAY DIFFRACTIONr_angle_other_deg0.69732251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
X-RAY DIFFRACTIONr_nbd_refined0.2230.3146
X-RAY DIFFRACTIONr_nbd_other0.2740.31206
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.5749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.5135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.383
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.452634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28331033
X-RAY DIFFRACTIONr_scbond_it1.6862391
X-RAY DIFFRACTIONr_scangle_it2.6643351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.602→1.687 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.231 84
Rwork0.2 1712
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6762-0.00361.11072.82251.04610.80410.0960.0339-0.06580.3333-0.0172-0.0780.07380.0093-0.07870.0896-0.0044-0.01830.02180.01010.030822.1992.67136.9339
23.87691.30.23171.28570.81191.2854-0.06280.06490.02050.0188-0.01740.08250.0691-0.02880.08020.03330.00030.0230.0538-0.00720.016911.3901-2.4637-2.3387
32.1348-1.0876-1.14034.4399-1.06440.7996-0.0538-0.02950.10620.25720.1757-0.0619-0.0497-0.0963-0.12190.04190.0080.00610.0217-0.00840.02832.40193.079725.9848
44.31262.12142.36241.51030.39892.71890.05770.019-0.1949-0.0409-0.0504-0.1193-0.05950.0497-0.00730.0285-0.00460.01560.0423-0.00670.018317.04158.296823.4352
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 311 - 31
2X-RAY DIFFRACTION2BB1 - 331 - 33
3X-RAY DIFFRACTION3CC1 - 311 - 31
4X-RAY DIFFRACTION4DD1 - 331 - 33

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